Gene loci information

Transcript annotation

  • This transcript has been annotated as Actin-5C.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_1 g14309 g14309.t4 isoform g14309.t4 36551443 36553062
chr_1 g14309 g14309.t4 exon g14309.t4.exon1 36551443 36552572
chr_1 g14309 g14309.t4 cds g14309.t4.CDS1 36551932 36552572
chr_1 g14309 g14309.t4 exon g14309.t4.exon2 36552714 36553062
chr_1 g14309 g14309.t4 cds g14309.t4.CDS2 36552714 36553062
chr_1 g14309 g14309.t4 TSS g14309.t4 NA NA
chr_1 g14309 g14309.t4 TTS g14309.t4 NA NA

Sequences

>g14309.t4 Gene=g14309 Length=1479
ATGTGTGACGAAGAAGTTGCTGCATTGGTCGTTGACAATGGATCAGGAATGTGCAAAGCC
GGTTTTGCTGGTGATGATGCACCACGTGCCGTTTTCCCATCAATTGTCGGTCGTCCACGT
CATCAAGGCGTTATGGTCGGTATGGGACAAAAGGACTCATATGTTGGTGATGAGGCTCAA
AGCAAAAGAGGTATTCTTACCTTGAAATATCCAATTGAACACGGTATTGTTACAAACTGG
GATGATATGGAAAAGATCTGGCATCATACTTTCTACAATGAACTCCGTGTTGCACCTGAA
GAACATCCAGTCTTGCTTACCGAAGCTCCATTAAATCCAAAAGCAAATCTTCCAATTTAC
GAAGGTTATGCTTTGCCACATGCTATCCTTCGTCTTGATTTGGCCGGTCGTGATTTGACA
GATTATTTGATGAAAATCTTAACCGAACGTGGATACTCATTCACAACCACTGCCGAACGT
GAAATTGTTCGTGATATCAAAGAAAAATTGTGCTATGTTGCACTTGACTTTGAACAAGAA
ATGGCAACAGCTGCTTCATCAAGCTCATTGGAGAAATCATATGAATTGCCTGATGGACAA
GTCATCACAATCGGAAATGAACGATTCCGTTGTCCAGAAGCATTGTTCCAGCCATCATTC
TTGGGTATGGAAGCATGTGGTATTCACGAGACAACATACAATTCAATCATGAAGTGTGAC
GTTGATATCCGTAAAGACTTGTATGCCAACACAGTCTTGTCAGGTGGCACAACAATGTAC
CCAGGTATCGCTGATCGTATGCAAAAGGAAATTACAGCATTAGCTCCATCAACAATGAAG
ATCAAAATTATTGCACCACCAGAACGTAAATACTCAGTCTGGATCGGAGGTTCAATTTTG
GCATCGCTCTCAACCTTCCAACAAATGTGGATCAGCAAACAAGAATATGATGAATCAGGC
CCATCAATTGTCCACAGAAAATGCTTCTAAATTAATTATAATTGTAATCAATTACCACCT
TTAAGTCGTCGACATCAAGATCTTCAACCACAGAAACTCAAAAGACAATTGCATTTTTCA
CAGTTGAAATTCCATTCATTACATTCCACCACTTACAACATCAACTTTAAGAAAACATGT
ATTGTCAAAAATATTTTTTGCTCTTTTCTTTTCTATTATGAAAACAACATTTAAATTTAA
TTTAATTATTATATTACACTACTTTCTCAAAGATCATGAATTTATCACTCAAAAAAAAAA
AATGTGCAGAAAATGAATAAAAAGAAAAAGCTTCAAATTTCAAATTCATATAAAATTTTT
CTTCTAATCTTCAATATAACGAAGAACAAAAAACAATTATTACTTAAAGTATTGAATGTA
ATGCACATTACTTACTCAACATATTTGTGAAAAAAATTTCAGATTGCTACTTACTGAAAA
AGAATAAAGACACATTTTCATTAAACATACAAAACGCTT

>g14309.t4 Gene=g14309 Length=329
MCDEEVAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQ
SKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANLPIY
EGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQE
MATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMEACGIHETTYNSIMKCD
VDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSIL
ASLSTFQQMWISKQEYDESGPSIVHRKCF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g14309.t4 CDD cd00012 NBD_sugar-kinase_HSP70_actin 9 137 3.60722E-7
14 g14309.t4 Gene3D G3DSA:3.30.420.40 - 1 115 4.2E-56
13 g14309.t4 Gene3D G3DSA:3.30.420.40 - 117 287 1.1E-78
12 g14309.t4 Gene3D G3DSA:3.90.640.10 Actin; Chain A 136 222 1.1E-78
15 g14309.t4 Gene3D G3DSA:3.30.420.40 - 288 327 4.2E-12
4 g14309.t4 PANTHER PTHR11937 ACTIN 3 116 2.9E-216
6 g14309.t4 PANTHER PTHR11937:SF192 ACTIN, CYTOPLASMIC 1 3 116 2.9E-216
3 g14309.t4 PANTHER PTHR11937 ACTIN 117 328 2.9E-216
5 g14309.t4 PANTHER PTHR11937:SF192 ACTIN, CYTOPLASMIC 1 117 328 2.9E-216
7 g14309.t4 PRINTS PR00190 Actin signature 27 36 4.4E-23
8 g14309.t4 PRINTS PR00190 Actin signature 50 61 4.4E-23
9 g14309.t4 PRINTS PR00190 Actin signature 62 84 4.4E-23
2 g14309.t4 Pfam PF00022 Actin 4 116 6.7E-38
1 g14309.t4 Pfam PF00022 Actin 118 329 4.4E-81
18 g14309.t4 ProSitePatterns PS00406 Actins signature 1. 54 64 -
17 g14309.t4 ProSitePatterns PS00432 Actins signature 2. 310 318 -
19 g14309.t4 SMART SM00268 actin_3 6 329 3.7E-182
10 g14309.t4 SUPERFAMILY SSF53067 Actin-like ATPase domain 5 117 3.39E-48
11 g14309.t4 SUPERFAMILY SSF53067 Actin-like ATPase domain 118 329 3.61E-91

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below. There were no conditions that were differentially expressed